I know to remove the countries from the DB but was wanting remove the actual folders in my root directory to clean things up and save a little space. Are their other references to those folders that may throw errors if they are removed?
Did you mean other country flags image in wwwroot\images\flags folder? Those flag images are being used mostly with Language not Country, you can check here. https://admin-demo.nopcommerce.com/Admin/Language/Edit/1 So you can keep you language related flag files and delete others.
Are these directories directly related to the language(s) installed If yes, can you delete the directories for a language if you are not using that language ?
I guess you could save about 5MB of disk space if it was possible ?